Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	239,378	G→A	pseudogene (273/273 nt)	yafF →	pseudogene, H repeat‑associated protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	239,378	0	G	A	100.0%	111.1 / NA	35	pseudogene (273/273 nt)	yafF	pseudogene, H repeat‑associated protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/18);  total (17/18)

TACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAATGCGC  >  NC_000913/239248‑239512                                                                                                                                   |                                                                                                                                       tACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATAccc                                                                                                                                >  1:585459/1‑139 (MQ=255)               aTTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtaata                                                                                                                                      <  1:1083518/119‑1 (MQ=18)                  aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCtt                                                                                                               <  1:845930/139‑1 (MQ=255)                  aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCCTAATAATACCCCGACTCTCCCCGTCCtt                                                                                                               <  1:933287/139‑1 (MQ=255)                      ttttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                                    >  1:708316/1‑130 (MQ=255)                      ttttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCg                                                                                                                    <  2:708316/130‑1 (MQ=255)                       tttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAACAATACCCCGACTCTccc                                                                                                                      >  1:1021811/1‑127 (MQ=255)                       tttGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTATCGTAATAATACCCCGACTCTccc                                                                                                                      <  2:1021811/127‑1 (MQ=255)                                       gTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTcacca                                                                                          <  2:1215538/139‑1 (MQ=255)                                          ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                                 <  2:17862/129‑1 (MQ=255)                                          ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                                 >  1:17862/1‑129 (MQ=255)                                           tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTa                                                                                                              <  2:1280909/115‑1 (MQ=255)                                           tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTa                                                                                                              >  1:1280909/1‑115 (MQ=255)                                           tCAACGCAGGGTTAAGACGTAAGATACGAAAAGCAGCCATGGACCGCAACTACCTGGCGCCAATCCTTGCGGAGAGCGGGCTTTCCTACTAACACCCCCACTCTCCCCGTCATTAAACACAACCCTCACTCACCaaaaa                                                                                      >  2:1249734/1‑138 (MQ=18)                                                  aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACt                                                                               >  1:825738/1‑139 (MQ=255)                                                  aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACt                                                                               >  1:1131066/1‑139 (MQ=255)                                                         aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                                     >  2:133533/1‑78 (MQ=17)                                                         aGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGtaataa                                                                                                                                     <  1:133533/78‑1 (MQ=12)                                                              tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                               >  1:3676/1‑111 (MQ=255)                                                              tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                               <  2:3676/111‑1 (MQ=255)                                                                aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                      >  2:545717/1‑86 (MQ=255)                                                                aGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTccc                                                                                                                      <  1:545717/86‑1 (MQ=255)                                                                     cGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACtctc                                                                                                                        >  1:1409062/1‑79 (MQ=255)                                                                     cGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACtctc                                                                                                                        <  2:1409062/79‑1 (MQ=255)                                                                             agcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACt                                                    <  2:585459/139‑1 (MQ=255)                                                                               ccATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGTCTCTCCCCGTCCTTAAACACAACCCCCACTCACCACACCCTAAACTCATCCGCATCCTGCCATGCCGGAAACttt                                                  <  2:1131066/139‑1 (MQ=255)                                                                                 aTGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTtc                                                <  2:91847/139‑1 (MQ=255)                                                                                         aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                               >  2:419111/1‑84 (MQ=255)                                                                                         aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACt                                                                                               <  1:419111/84‑1 (MQ=255)                                                                                         aaaCTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATAtt                                        >  2:97946/1‑139 (MQ=255)                                                                                                    cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                                 <  2:442856/71‑1 (MQ=255)                                                                                                    cGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCa                                                                                                 >  1:442856/1‑71 (MQ=255)                                                                                                       cAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACt                                                                               <  2:1340865/86‑1 (MQ=255)                                                                                                       cAGTCCTTGCGGGGAGCGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACt                                                                               >  1:1340865/1‑86 (MQ=255)                                                                                                                       cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                         <  2:127619/44‑1 (MQ=255)                                                                                                                       cGGGCTTTCGTAATAATACCCCGACTCTCCCCGTCCTTAAacac                                                                                                         >  1:127619/1‑44 (MQ=255)                                                                                                                               cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAcct                                                                                                    <  2:940616/41‑2 (MQ=255)                                                                                                                               cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAAccc                                                                                                    >  1:940616/1‑41 (MQ=255)                                                                                                                               cGTAATAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCTACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAATgcgc  >  1:985997/1‑139 (MQ=255)                                                                                                                                   |                                                                                                                                       TACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTAAACACAACCCCCACTCACCACAACCTAAACTCATCCGCATCCTGCCATGCCGGAAACTTTTCTCTATATTCCCGCAATGCTGCCATCGACAGCTCCGCATCAATGCGC  >  NC_000913/239248‑239512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑